Issues

• Use All Cores by Default in Scanpy-Scripts

  ebi-gene-expression-group/scanpy-scripts#137 · Filter by author anilthanki opened on Jan 14, 2025
  3

• Scrublet failing on certain dataset

  ebi-gene-expression-group/scanpy-scripts#134 · Filter by author anilthanki opened on May 31, 2024

• Highly variable genes calculations should allow to blacklist or white list specific subset of genes

  ebi-gene-expression-group/scanpy-scripts#129 · Filter by author pcm32 opened on Feb 12, 2024

• Scrublet double prediction fails with cells with under 5 expressed genes

  ebi-gene-expression-group/scanpy-scripts#125 · Filter by author pcm32 opened on Jan 23, 2024

• Scrubblet module fails when running with less than 30 cells

  ebi-gene-expression-group/scanpy-scripts#124 · Filter by author pcm32 opened on Oct 30, 2023

• Using a single group in find marker genes fails

  ebi-gene-expression-group/scanpy-scripts#123 · Filter by author pcm32 opened on Apr 20, 2023

• Add filtering by quantiles

  ebi-gene-expression-group/scanpy-scripts#122 · Filter by author pcm32 opened on Mar 27, 2023

• PlotEmbedd could give more user friendly errors to allow users to recover

  ebi-gene-expression-group/scanpy-scripts#121 · Filter by author pcm32 opened on Mar 10, 2023

• Should we add ability to mark ribosomal genes?

  ebi-gene-expression-group/scanpy-scripts#119 · Filter by author pcm32 opened on Nov 18, 2022

• How can I use scanpy_scripts?

  ebi-gene-expression-group/scanpy-scripts#118 · Filter by author cooperist opened on Oct 9, 2022
  3

• Calculations of mito directly generate columns with dtypes that break qc calculations on subsequent filtering

  ebi-gene-expression-group/scanpy-scripts#116 · Filter by author pcm32 opened on Sep 21, 2022
  3

• Problems with Python 3.9.* - umap-learn<0.4.0 needed?

  ebi-gene-expression-group/scanpy-scripts#102 · Filter by author LustigePerson opened on Jul 12, 2021
  3